Compositions and methods for sequencing nucleic acids

1. A method of amplifying deletion products on a solid surface, said method comprising:

providing a plurality of polynucleotides;

processing said plurality of polynucleotides by one or more of i) incompletely extending a capture probe, ii) physically shearing a full length a full length polynucleotide, and/or iii) digesting a full length polynucleotide thereby generating an overlapping set of deletion products and amplifying said set of deletion products on the surface to form amplicons corresponding to the set of deletion products, so as to produce a set of overlapping nucleotide regions to be sequenced;

providing a substrate having a surface, said surface comprising a site having said set of overlapping nucleotide regions attached thereto; and

sequencing said set of overlapping nucleotide regions, thereby generating a set of overlapping sequencing reads.

2. A method of amplifying deletion products on a solid surface comprising:

providing a substrate having a surface, said surface comprising a site having a plurality of polynucleotides attached thereto;

generating deletion products from said plurality of polynucleotides by one or more of i) incompletely extending a capture probe, ii) physically shearing a full length a full length polynucleotide, and/or iii) digesting a full length polynucleotide thereby generating an deletion products;

amplifying the deletion products on the surface to form amplicons corresponding to the deletion products; and

obtaining nucleotide sequence information from nucleic acids present in said amplicons.

3. The method of claim 2 , wherein said deletion products comprise overlapping deletion products.

4. The method of claim 3 further comprising the step of assembling nucleotide sequence information corresponding to said overlapping deletion products, thereby producing a contiguous nucleotide sequence of a nucleic acid of interest.

5. The method of claim 2 , wherein providing said substrate comprises hybridizing a plurality of template nucleic acids to a plurality of primers attached to said site.

6. The method of claim 5 , wherein each template nucleic acid comprises an adaptor sequence that is complementary to a primer sequence.

7. The method of claim 6 , wherein said plurality of primers comprises first primers and second primers, said first primers and said second primers comprising a different nucleotide sequence.

8. The method of claim 5 further comprising extending said primers, thereby producing extended strands.

9. The method of claim 8 further comprising preamplifying said extended strands prior to generating deletion products.

10. The method of claim 5 , wherein generating deletion products comprises extending said primers in the presence of one or more terminator nucleotides such that said primers are extended to lengths that are less than the full length of the template nucleic acid.

11. The method of claim 10 further comprising dehybridizing said template nucleic acids, thereby producing single-stranded deletion products.

12. The method of claim 11 further comprising attaching an adaptor to a free end of the single-stranded deletion products.

13. The method of claim 5 , wherein generating deletion products comprises extending said primers in the presence of uracil such that said primers are extended to lengths that are less than the full length of the template nucleic acid.

14. The method of claim 2 , wherein generating deletion products comprises digesting said plurality of polynucleotides with an exonuclease.

15. The method of claim 2 , wherein generating deletion products comprises physically shearing said polynucleotides.

16. The method of claim 2 , wherein said polynucleotides comprise double-stranded polynucleotides having a nick and generating deletion products comprises translating said nick less than the full length of the polynucleotides and cleaving at said nick.

17. The method of claim 2 , wherein said deletion products comprise an oligonucleotide tag.

18. The method of claim 17 , wherein said oligonucleotide tag is complementary to a sequencing primer.

19. The method of claim 2 , wherein the substrate comprises a flow chamber.

20. The method of claim 2 , wherein the surface is planar.

21. The method of claim 2 , wherein the surface is patterned.

22. The method of claim 2 , wherein the surface comprises a channel in a flow chamber.

23. The method of claim 2 , wherein said site comprises a well.

24. The method of claim 2 , wherein said site comprises a bead in a well.